Ronaldo appeared as a first half substitute for the injured Anthony Martial to score the winner in a 2-1 victory at Goodison Park.
It was Ronaldo's second goal of the season and his first in the Premier League this term as United moved to fifth on the table.
The Portugal captain has now tallied 700 goals in his club career, including five for Sporting Lisbon, 144 across two spells with Manchester United, 450 for Real Madrid and 101 for Juventus.
Ronaldo also holds the record for the most international goals in men's football, having struck 117 times for Portugal.
"It is tough still counting goals for Cristiano because every week it seems like a new record," Fernandes told BT Sport about the 37-year-old.
"We're really happy because he has been working hard to get this goal, we saw it last Thursday, it was tough for him. Today he got the goal and the win.
"That's most important for Cristiano, I think, that the team wins, and obviously as a striker he wants to score goals and we are really happy for that."
United fell behind to Alex Iwobi's fifth minute strike before Antony levelled matters ten minutes later with his third Premier League goal in as many games.
Manager Erik Ten Hag was glad with the reaction of his side after going behind so early in the game.
"We were quickly 1-0 down but the reaction of the team was good," Ten Hag told BT Sport.
"One of our aims is to deal better with setbacks and they stayed composed. It was quite impressive from our side.
"In the first half we were pressing well. Everton did not come out and it was difficult for them to get a lot of crosses in, we didn't allow them and I am happy with that.
"Casemiro will anticipate quickly, and we saw during the game how important he is, winning a lot of balls. He also played the ball for the goal from Cristiano Ronaldo. He grew into the game.
"Once again, we were happy with all the subs, Ronaldo coming on and getting the winning goal, and Rapha [Varane] showed his importance with his organisation and heading capacity."
